Establishing appropriate diagnostic characters for taxonomic delineation is critical for the reliable classification and organization of life. Yet in most ciliate research, taxonomic characters and species boundaries are largely ambiguous. Implications for this include our ability to estimate patterns of global protist biodiversity, and our understanding of the ecological and evolutionary processes that govern these patterns. The following work evaluates the diagnostic characters and indices of identification in marine ciliates through the incorporation of both traditional and contemporary methods. Patterns and processes of marine protist diversity are interpreted using contemporary studies, which reveal evidence for endemism, widespread crypticity, impermanent barriers to gene flow, and high diversity at both local and global scales. The mechanisms of diversification that create and maintain these patterns are explored, including rapid speciation events, allopatry, epigenetics, and the incorporation of existing evolutionary frameworks once reserved only for multicellular life. Currently, the suggested diagnostic characters used to inform taxonomic delineation in ciliates include a combination of morphologic, genetic, and ecological data. These characters are used to describe the new genus and species Dartintinnus alderae (class Spirotrichea, order Tintinnida), which is delineated from all described ciliates through unique morphologic features, a substantial genetic divergence in barcode regions, and the tendency to persist in brackish waters.